I'm pretty sure I can put the main body together but I'm not sure what to for the fluffy white part around the neck and hood. I didnt want to just thought cotton balls on it, I want to keep that pajama look that you could just sleep in.

Also I'm not sure how to make the ball at the end of the tail. I dont want the ball to be made out of fabric.

I would make the swirls out of fleece. you could stitch the swirls into an almost hood-shaped pattern with batting between the two layers of fleece to keep them fluffier between the lines of stitching. You could even do two or three segments like this (with almost scalloped edging) and overlap them to form the hood shape.

I have come up with a new problem! The tail on Flaaffy does not hang down but sticks up. I've heard of putting wire through it but think it would still just fall over. Is there any other ideas? The look I'm going for is cute pajamas, I want to be able to lay down and curl up without worrying about the tail hurting me or breaking.

If you stuff the tail enough it will become rigid enough to hold shape. However it may still flop some just because its being attached to a loose area, the stitch line will act as a sort of hinge. There really isn't anything you can do to solve this, any extra weight added via wire or another means will simply weigh down the butt of the suit.

I would suggest making the tail smaller, maybe max a foot, as a general idea of the tail without it being full sized. After all these are PJs not a fursuit or anything like that so you have some leeway to things like that. Another thing that might help is instead of sewing it flat into a seam sew it on by hand so the base of the tail remains circular.